Search NASA⌕ Search

SEARCH · Search NASA

Results for “CASP”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Modeling SARS-CoV-2 proteins in the CASP-commons experiment

Critical Assessment of Structure Prediction (CASP) is an organization aimed at advancing the state of the art in computing protein structure from sequence. In the spring of 2020, CASP launched a community project to compute the structures of the most structurally challenging proteins coded for in the SARS-CoV-2 genome. Forty-seven research groups submitted over 3000 three-dimensional models and 700 sets of accuracy estimates on 10 proteins. The resulting models were released to the public. CASP community members also worked together to provide estimates of local and global accuracy and identify structure-based domain boundaries for some proteins. Subsequently, two of these structures (ORF3a and ORF8) have been solved experimentally, allowing assessment of both model quality and the accuracy estimates. Models from the AlphaFold2 group were found to have good agreement with the experimental structures, with main chain GDT_TS accuracy scores ranging from 63 (a correct topology) to 87 (competitive with experiment).

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1988

Center for Advanced Space Propulsion (CASP)

With a mission to initiate and conduct advanced propulsion research in partnership with industry, and a goal to strengthen U.S. national capability in propulsion technology, the Center for Advanced Space Propulsion (CASP) is the only NASA Center for Commercial Development of Space (CCDS) which focuses on propulsion and associated technologies. Meetings with industrial partners and NASA Headquarters personnel provided an assessment of the constraints placed on, and opportunities afforded commercialization projects. Proprietary information, data rights, and patent rights were some of the areas where well defined information is crucial to project success and follow-on efforts. There were five initial CASP projects. At the end of the first year there are six active, two of which are approaching the ground test phase in their development. Progress in the current six projects has met all milestones and is detailed. Working closely with the industrial counterparts it was found that the endeavors in expert systems development, computational fluid dynamics, fluid management in microgravity, and electric propulsion were well received. One project with the Saturn Corporation which dealt with expert systems application in the assembly process, was placed on hold pending further direction from Saturn. The Contamination Measurment and Analysis project was not implemented since CASP was unable to identify an industrial participant. Additional propulsion and related projects were investigated during the year. A subcontract was let to a small business, MicroCraft, Inc., to study rocket engine certification standards. The study produced valuable results; however, based on a number of factors it was decided not to pursue this project further.

Source record↗
DOE OSTI2020

The Consortium for Advanced Sorghum Phenomics (CASP). Final report

The goal of CASP was to accelerate breeding of biomass sorghum [Sorghum bicolor (L.) Moench] by identifying genotypes exhibiting high yield under well-watered, pre- or post-drought and/or salinity-stress conditions. We did this by combining high-throughput, non-invasive drone phenotyping with genomics and molecular profiling. Field-based phenotyping utilized a multi-modal sensor suite of LiDAR, multispectral cameras, and thermal cameras mounted on a commercial drone to detect traits required for yield prediction and selection of drought and saline tolerant lines of sorghum. Traits of interest included plant height (PH), leaf area index (LAI), wet biomass (BMW), and biomass at 65% moisture (BM65) and were measured from emergence to harvest on a weekly basis over three growing seasons. The final output were measurements of traits on a plot-by-plot basis, identified by the plot ID used by the Proprietary data processing software enabled raw field data to be turned into plant traits and delivered to the PNNL and JGI within the same workday.

09 BIOMASS FUELS↗
NASA NTRS1990

Establishing a center for advanced space propulsion

The goals and the concept of NASA-sponsored Centers for the Commercial Development of Space (CCDSs) are presented. The Center for Advanced Space Propulsion (CASP), its research projects, and the prognosis for their success are discussed. The establishment of CCDSs is recognized as an experiment to bring together university and industry researchers to maintain and improve the internationally competitive position of the United States in space. Increasing private investment in space-related technology and developing new commercial products are the basic requirements for success. CASP is the only CCDS that focuses on propulsion technology, which is critical to ensuring continued U.S. leadership in space. CASP is expected to become a recognized center for propulsion research and commercialization within the next five years.

Garrison, George W.↗
DOE OSTI2021

Prediction of protein assemblies, the next frontier: The CASP14-CAPRI experiment

Here we present the results for CAPRI Round 50, the fourth joint CASP-CAPRI protein assembly prediction challenge. The Round comprised a total of twelve targets, including six dimers, three trimers, and three higher-order oligomers. Four of these were easy targets, for which good structural templates were available either for the full assembly, or for the main interfaces (of the higher-order oligomers). Eight were difficult targets for which only distantly related templates were found for the individual subunits. Twenty-five CAPRI groups including eight automatic servers submitted ~1250 models per target. Twenty groups including six servers participated in the CAPRI scoring challenge submitted ~190 models per target. The accuracy of the predicted models was evaluated using the classical CAPRI criteria. The prediction performance was measured by a weighted scoring scheme that takes into account the number of models of acceptable quality or higher submitted by each group as part of their five top-ranking models. Compared to the previous CASP-CAPRI challenge, top performing groups submitted such models for a larger fraction (70–75%) of the targets in this Round, but fewer of these models were of high accuracy. Scorer groups achieved stronger performance with more groups submitting correct models for 70–80% of the targets or achieving high accuracy predictions. Servers performed less well in general, except for the MDOCKPP and LZERD servers, who performed on par with human groups. In addition to these results, major advances in methodology are discussed, providing an informative overview of where the prediction of protein assemblies currently stands.

protein complexes↗
DOE OSTI2021

Structural analysis of the catalytic domain of Artemis endonuclease/SNM1C reveals distinct structural features

The endonuclease Artemis is responsible for opening DNA hairpins during V(D)J recombination and for processing a subset of pathological DNA double-strand breaks. Artemis is an attractive target for the development of therapeutics to manage various B cell and T cell tumors, because failure to open DNA hairpins and accumulation of chromosomal breaks may reduce the proliferation and viability of pre-T and pre-B cell derivatives. However, structure-based drug discovery of specific Artemis inhibitors has been hampered by a lack of crystal structures. Here, we report the structure of the catalytic domain of recombinant human Artemis. The catalytic domain displayed a polypeptide fold similar overall to those of other members in the DNA cross-link repair gene SNM1 family and in mRNA 3'-end-processing endonuclease CPSF-73, containing metallo-β-lactamase and β-CASP domains and a cluster of conserved histidine and aspartate residues capable of binding two metal atoms in the catalytic site. As in SNM1A, only one zinc ion was located in the Artemis active site. However, Artemis displayed several unique features. Unlike in other members of this enzyme class, a second zinc ion was present in the β-CASP domain that leads to structural reorientation of the putative DNA-binding surface and extends the substrate-binding pocket to a new pocket, pocket III. Moreover, the substrate-binding surface exhibited a dominant and extensive positive charge distribution compared with that in the structures of SNM1A and SNM1B, presumably because of the structurally distinct DNA substrate of Artemis. The structural features identified here may provide opportunities for designing selective Artemis inhibitors.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1990

The subscale orbital fluid transfer experiment

The Subscale Orbital Fluid Transfer Experiment (SOFTE) is a planned Shuttle Orbiter fluid transfer experiment. CASP (Center for Advanced Space Propulsion) performed certain aspects of the conceptual design of this experiment. The CASP work consisted of the conceptual design of the optical system, the search for alternative experimental fluids, the determination of the flow meter specifications and the examination of materials to use for a bladder that will empty one of the tanks in the experiment.

Collins, Frank G.↗
DOE OSTI2023

An examination of the metal ion content in the active sites of human endonucleases CPSF73 and INTS11

Human cleavage and polyadenylation specificity factor (CPSF)73 (also known as CPSF3) is the endoribonuclease that catalyzes the cleavage reaction for the 3'-end processing of pre-mRNAs. The active site of CPSF73 is located at the interface between a metallo-β-lactamase domain and a β-CASP domain. Two metal ions are coordinated by conserved residues, five His and two Asp, in the active site, and they are critical for the nuclease reaction. The metal ions have long been thought to be zinc ions, but their exact identity has not been examined. Here we present evidence from inductively coupled plasma mass spectrometry and X-ray diffraction analyses that a mixture of metal ions, including Fe, Zn, and Mn, is present in the active site of CPSF73. The abundance of the various metal ions is different in samples prepared from different expression hosts. Zinc is present at less than 20% abundance in a sample expressed in insect cells, but the sample is active in cleaving a pre-mRNA substrate in a reconstituted canonical 3'-end processing machinery. Zinc is present at 75% abundance in a sample expressed in human cells, which has comparable endonuclease activity. We also observe a mixture of metal ions in the active site of the CPSF73 homolog INTS11, the endonuclease for Integrator. Taken together, our results provide further insights into the role of metal ions in the activity of CPSF73 and INTS11 for RNA 3'-end processing.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Discovery of hybrid chemical synthesis pathways with DORAnet

Developing efficient tools for discovering novel synthesis pathways is essential to advance chemical production methods that maximize the use of resources and energy. We introduce DORAnet (Designing Optimal Reaction Avenues Network Enumeration Tool), an open-source computational framework that addresses key limitations in current computer-aided synthesis planning (CASP) tools. DORAnet integrates both chemical/chemocatalytic (i.e., non-enzymatic) and enzymatic transformations, enabling the discovery of hybrid synthesis pathways. With 390 expert-curated chemical/chemocatalytic reaction rules and 3606 enzymatic rules derived from MetaCyc, it provides extensive flexibility for synthetic chemists and biotechnologists. The framework features customizable network expansion strategies, advanced filtering, and pathway search, ranking, and visualization tools. Validated against known reaction data, DORAnet successfully identified both established and novel synthesis routes for key industrial chemicals. In a case study involving 51 high-volume targets, DORAnet frequently ranked known commercial pathways among the top three results, demonstrating its practical relevance and ranking accuracy, while also uncovering numerous alternative (hybrid) synthesis pathways that were highly ranked.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

A deep dilated convolutional residual network for predicting interchain contacts of protein homodimers

Abstract Motivation Deep learning has revolutionized protein tertiary structure prediction recently. The cutting-edge deep learning methods such as AlphaFold can predict high-accuracy tertiary structures for most individual protein chains. However, the accuracy of predicting quaternary structures of protein complexes consisting of multiple chains is still relatively low due to lack of advanced deep learning methods in the field. Because interchain residue–residue contacts can be used as distance restraints to guide quaternary structure modeling, here we develop a deep dilated convolutional residual network method (DRCon) to predict interchain residue–residue contacts in homodimers from residue–residue co-evolutionary signals derived from multiple sequence alignments of monomers, intrachain residue–residue contacts of monomers extracted from true/predicted tertiary structures or predicted by deep learning, and other sequence and structural features. Results Tested on three homodimer test datasets (Homo_std dataset, DeepHomo dataset and CASP-CAPRI dataset), the precision of DRCon for top L/5 interchain contact predictions (L: length of monomer in a homodimer) is 43.46%, 47.10% and 33.50% respectively at 6 Å contact threshold, which is substantially better than DeepHomo and DNCON2_inter and similar to Glinter. Moreover, our experiments demonstrate that using predicted tertiary structure or intrachain contacts of monomers in the unbound state as input, DRCon still performs well, even though its accuracy is lower than using true tertiary structures in the bound state are used as input. Finally, our case study shows that good interchain contact predictions can be used to build high-accuracy quaternary structure models of homodimers. Availability and implementation The source code of DRCon is available at https://github.com/jianlin-cheng/DRCon. The datasets are available at https://zenodo.org/record/5998532#.YgF70vXMKsB. Supplementary information Supplementary data are available at Bioinformatics online.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Identification of Novel Genomic Associations and Gene Candidates for Grain Starch Content in Sorghum

Starch accumulated in the endosperm of cereal grains as reserve energy for germination serves as a staple in human and animal nutrition. Unraveling genetic control for starch metabolism is important for breeding grains with high starch content. In this study, we used a sorghum association panel with 389 individuals and 141,557 single nucleotide polymorphisms (SNPs) to fit linear mixed models (LMM) for identifying genomic regions and potential candidate genes associated with starch content. Three associated genomic regions, one in chromosome (chr) 1 and two novel associations in chr-8, were identified using combination of LMM and Bayesian sparse LMM. All significant SNPs were located within protein coding genes, with SNPs ∼ 52 Mb of chr-8 encoding a Casperian strip membrane protein (CASP)-like protein (Sobic.008G111500) and a heat shock protein (HSP) 90 (Sobic.008G111600) that were highly expressed in reproductive tissues including within the embryo and endosperm. The HSP90 is a potential hub gene with gene network of 75 high-confidence first interactors that is enriched for five biochemical pathways including protein processing. The first interactors of HSP90 also showed high transcript abundance in reproductive tissues. The candidates of this study are likely involved in intricate metabolic pathways and represent candidate gene targets for source-sink activities and drought and heat stress tolerance during grain filling.

genomics↗
DOE OSTI2022

Homologs of Phycobilisome Abundance Regulator PsoR Are Widespread across Cyanobacteria

During chromatic acclimation (CA), cyanobacteria undergo shifts in their physiology and metabolism in response to changes in their light environment. Various forms of CA, which involves the tuning of light-harvesting accessory complexes known as phycobilisomes (PBS) in response to distinct wavelengths of light, have been recognized. Recently, a negative regulator of PBS abundance, PsoR, about which little was known, was identified. We used sequence analyses and bioinformatics to predict the role of PsoR in cyanobacteria and PBS regulation and to examine its presence in a diverse range of cyanobacteria. PsoR has sequence similarities to the β-CASP family of proteins involved in DNA and RNA processing. PsoR is a putative nuclease widespread across Cyanobacteria, of which over 700 homologs have been observed. Promoter analysis suggested that psoR is co-transcribed with upstream gene tcpA. Multiple transcription factors involved in global gene regulation and stress responses were predicted to bind to the psoR-tcpA promoter. The predicted protein–protein interactions with PsoR homologs included proteins involved in DNA and RNA metabolism, as well as a phycocyanin-associated protein predicted to interact with PsoR from Fremyella diplosiphon (FdPsoR). The widespread presence of PsoR homologs in Cyanobacteria and their ties to DNA- and RNA-metabolizing proteins indicated a potentially unique role for PsoR in CA and PBS abundance regulation.

Layer, Alicia↗
NASA NTRS1990

New instruments for solar research

In fulfilment of its goal to develop early detection and warning of emerging solar magnetic fields, the Center for Applied Solar Physics (CASP) has designed and constructed a solar vector magnetograph (VMG) that will provide unique data on the sunspot regions where flares originate. The instrument is reportedly beginning to approach its goals of measuring all three components of the solar magnetic field with a sensitivity of 50 to 100 G and a spatial resolution on the sun of about 700 km (1 arcsec). Importance of new high-resolution capabilities is stressed and the interpretation of VMG measurements is discussed. The performance of the solar VMG, installed in a 6-m dome at the National Solar Observatory at Sacramento Peak in Sunspot, New Mexico, and its construction and environment are described; particular attention is given to the use and function of the filters. Initial results are examined, including a description and analysis of a magnetogram obtained after installation of an improved blocking filter.

Rust, David M.↗
NASA NTRS1995

Center for Advanced Space Propulsion

The Center for Advanced Space Propulsion (CASP) is part of the University of Tennessee-Calspan Center for Aerospace Research (CAR). It was formed in 1985 to take advantage of the extensive research faculty and staff of the University of Tennessee and Calspan Corporation. It is also one of sixteen NASA sponsored Centers established to facilitate the Commercial Development of Space. Based on investigators' qualifications in propulsion system development, and matching industries' strong intent, the Center focused its efforts in the following technical areas: advanced chemical propulsion, electric propulsion, AI/Expert systems, fluids management in microgravity, and propulsion materials processing. This annual report focuses its discussion in these technical areas.

Source record↗
NASA NTRS1995

Advanced high area ratio nozzles

The objective is to develop computational techniques for the design of high-area-ratio nozzles and to validate these models by comparison with experiments and computations using other codes. Progress was made in two areas during the past year. First, performance computations were added to the PARC2D code and the performance of the SSME nozzle was computed for inviscid, laminar and turbulent flow assuming a perfect gas with gamma = 1.2. Second, the PARC2D code was modified in a non-CASP project to compute equilibrium flow about hypersonic blunt bodies. Progress has been made toward modifying this code to compute equilibrium H2/O2 flow through the SSME and related nozzles.

Raiszadeh, Farhad↗
NASA NTRS1989

Overview of the Center for Advanced Space Propulsion

The mission of the Center for Advanced Space Propulsion (CASP), a Center for the Commercial Development of Space (CCDS), is to strengthen U.S. competitiveness in space technology, foster cooperative research with industry and government, assist industry in developing commercial products and services, and perform research in advanced space propulsion. Current areas of focus are (1) advanced chemical propulsion, including high area ratio nozzle performance, variable thrust engine performance, and spray combustion stability; (2) artificial intelligence propulsion applications, including health monitoring of rocket engines, fault pattern detection and diagnosis, and intelligent hypertext applications; (3) microgravity fluid management, including liquid storage and transfer, a subscale orbital fluid transfer experiment, and helical, two-phase flow; (4) electric propulsion, including magnetic annular arc thruster, ion thrustor, and electrostatic plasma accelerator; and (5) laser materials processing.

George W Garrison↗
NASA NTRS1989

Advanced high area ratio nozzles

The objective is to develop computational techniques for the design of high-area-ratio nozzles and to validate these models by comparison with experiments and computations using other codes. Performance computations were added to the PARC2D code and the performance of the space shuttle main engine (SSME) nozzle was computed for inviscid, laminar and turbulent flow assuming a perfect gas with gamma = 1.2. The PARC2D code was modified in a non-CASP (Center for Advanced Space Propulsion) project to compute equilibrium flow about hypersonic blunt bodies. Progress has been made toward modifying this code to compute equilibrium H2/O2 flow through the SSME and related nozzles.

Raiszadeh, Farhad↗